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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "70%"
)
```
# concordexR
<!-- badges: start -->
[](https://codecov.io/gh/pachterlab/concordexR)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/concordexR)
<!-- badges: end -->
The goal of concordexR is to identify spatial homogeneous regions (SHRs) as
defined in the recent manuscript, ["Identification of spatial homogenous regions in tissues with concordex"](https://doi.org/10.1101/2023.06.28.546949). Briefly, SHRs are are
domains that are homogeneous with respect to cell type composition. `concordex`
relies on the the k-nearest-neighbor (kNN) graph to representing similarities
between cells and uses common clustering algorithms to identify SHRs.
## Installation
Versions of the `concordexR` package that do not enable clustering spatial data
into spatial homogeneous regions (SHRs) are available for Bioconductor versions
3.17-19. The most recent version of the package is slated to be released on
Bioconductor version 3.20.
```{r}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version="3.20")
BiocManager::install("concordexR")
```
## Example
This is a basic example using concordex:
```{r load libraries}
library(SFEData)
library(Voyager)
library(scran)
library(bluster)
library(concordexR)
```
```{r}
sfe <- McKellarMuscleData("small")
clusters <- quickCluster(sfe, min.size=2, d=15)
```
```{r example}
nbc <- calculateConcordex(
sfe,
clusters,
n_neighbors=10,
BLUSPARAM=KmeansParam(2)
)
colData(sfe)[["shr"]] <- attr(nbc, "shrs")
```
```{r plot-shr}
plotSpatialFeature(sfe, features="shr")
```
## Citation
If you'd like to use the `concordexR` package in your research, please cite our
recent bioRxiv preprint
> Jackson, K.; Booeshaghi, A. S.; Gálvez-Merchán, Á.; Moses, L.; Chari, T.; Pachter, L. Quantitative assessment of single-cell RNA-seq clustering with CONCORDEX. bioRxiv (Cold Spring Harbor Laboratory) 2023. https://doi.org/10.1101/2023.06.28.546949.
> @article {Jackson2023.06.28.546949,
author = {Jackson, Kayla C. and Booeshaghi, A. Sina and G{\'a}lvez-Merch{\'a}n, {\'A}ngel and Moses, Lambda and Chari, Tara and Kim, Alexandra and Pachter, Lior},
title = {Identification of spatial homogeneous regions in tissues with concordex},
year = {2024},
doi = {10.1101/2023.06.28.546949},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2024/07/18/2023.06.28.546949},
journal = {bioRxiv}
}
## Maintainer
[Kayla Jackson](https://github.com/kayla-jackson)